Stress and recovery, natural variation, gene expression and QTL

C. elegans serves as an important model for integrative analysis of stress
response. Analyzing the transcriptional regulation of stress response and
subsequent recovery provides insight into the mechanisms of fitness
optimization. Although C. elegans stress responses are well studied, the
recovery from stress is poorly understood. We investigated the
transcriptional response over the course of a heat-shock experiment in fully
sequenced recombinant inbred lines (RILs). This allowed us to identify
regulatory loci for stress recovery.
The RILs, derived from a cross between N2 and CB4856, were exposed to
heat-shock after which they were allowed to recover. In both environments,
and in a control environment (no heat stress), genome-wide expression
levels were measured. We then performed expression quantitative trait loci
(eQTL) mapping across these three environments to identify regulatory loci
that contribute to the recovery response.
Across all RILs the largest difference in gene expression was found
between control and heat-shock. Recovering populations showed patterns of
gene expression that were in-between the control and heat-shock. Some
RILs had a more control-like gene expression phenotype while other RILs
were more heat-shock-like, thus allowing for mapping of loci regulating
genetic variation in recovery. We found that genetic variation in gene
expression was largely independent of the environment. More specifically,
approximately 50% of the eQTL were similar in location and effect over the
three environments; therefore did not display interaction with the
environment. Only 1% of the genes with an eQTL in all environments
displayed environment-specific interaction. The remainder of the eQTL
with an environment-specific interaction were specifically detected in one
environment.
In conclusion, the combination of natural variation and gene expression
over the course of a stress response allows for mapping loci underlying
regulation in this response. The genes with an eQTL displaying
environment interaction are specific for one environment. Incorporation of
environment interactions facilitates specifying groups of related eQTL and
thereby allows for detailed eQTL network analysis.